Post-Transcriptional Gene Regulation

Preface.- Contributors.- I: Bioinformatics.- Bioinformatics Approaches for Studying Untranslated Regions of mRNAsParamjeet S. Bagga.- Identification of mRNA Polyadenylation Sites in Genomes Using cDNA Sequences, Expressed Sequence Tags, and TraceJu Youn Lee, Ji Yeon Park, and Bin Tian.- Bioinformatic Tools for Studying Post-Transcriptional Gene Regulation: The UAlbany TUTR Collection and Other Informatic ResourcesFrancis Doyle, Christopher Zaleski, Ajish D. George, Erin K. Stenson, Adele Ricciardi, and Scott A. Tenenbaum.- II: Fundamental Aspects of the Study of RNA Biology.- In-Line Probing Analysis of RiboswitchesElizabeth E. Regulski and Ronald R. Breaker.- Ribotrap: Targeted Purification of RNA-Specific RNPs from Cell Lysates Through Immunoaffinity Precipitation to Identify Regulatory Proteins and RNAsDale L. Beach and Jack D. Keene.- Advances in RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray ProfilingTimothy E. Baroni, Sridar V. Chittur, Ajish D. George, and Scott A. Tenenbaum.- Biosensors for RNA Aptamers—Protein InteractionSara Tombelli, Maria Minunni, and Marco Mascini.- A Tethering Approach to Study Proteins that Activate mRNA Turnover in Human CellsSandra L. Clement and Jens Lykke-Andersen.- RNA Analysis by Biosynthetic Tagging Using 4-Thiouracil and Uracil PhosphoribosyltransferaseGusti M. Zeiner, Michael D. Cleary, Ashley E. Fouts, Christopher D. Meiring, Edward S. Mocarski, and John C. Boothroyd.- Efficient 5? Cap-Dependent RNA Purification: Use in Identifying and Studying Subsets of RNAEdyta Z. Bajak and Curt H. Hagedorn.- III: Techniques for Specific Aspects of RNA Biology.- Enrichment of Alternatively Spliced IsoformsJulian P. Venables.- In Vivo Methods to Assess Polyadenylation EfficiencyLisa K. Hague, Tyra Hall-Pogar, andCarol S. Lutz.- Monitoring the Temporal and Spatial Distribution of RNA in Living Yeast CellsRoy M. Long and Carl R. Urbinati.- Analysis of mRNA Partitioning Between the Cytosol and Endoplasmic Reticulum Compartments of Mammalian CellsSamuel B. Stephens, Rebecca D. Dodd, Rachel S. Lerner, Brook M. Pyhtila, and Christopher V. Nicchitta.- In Vivo and In Vitro Analysis of Poly(A) Length Effects on mRNA TranslationJing Peng, Elizabeth L. Murray, and Daniel R. Schoenberg.- A Ribosomal Density-Mapping Procedure to Explore Ribosome Positions Along Translating mRNAsNaama Eldad and Yoav Arava.- Identification of Changes in Gene Expression by Quantitation of mRNA LevelsWendy M. Olivas.- Application of the Invader® RNA Assay to the Polarity of Vertebrate mRNA DecayElizabeth L. Murray and Daniel R. Schoenberg.- Development of an In Vitro mRNA Decay System in Insect CellsKevin Sokoloski, John R. Anderson, and Jeffrey Wilusz.- Using Synthetic Precursor and Inhibitor miRNAs to Understand miRNA FunctionLance P. Ford and Angie Cheng.- A Step-by-Step Procedure to Analyze the Efficacy of siRNA Using Real-Time PCRAngie Cheng, Charles L. Johnson, and Lance P. Ford.